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Primer removal in amplicon sequencing

Hello,

I am currently working with 16s and ITS amplicon sequencing data. I am processing this following DADA2 pipeline. I got the primer sequence for 16S as:

16S Amplicon PCR Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG

16S Amplicon PCR Reverse Primer = 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC

I think these have the overhang portion with the gene specific part. When I search for primers should I input the whole sequence or just the gene specific part? Because for full sequence search I get no primer hit, but for gene specific part I do get primer hits. Thanks!

removal primer amplicon dada2 sequencing
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updated by GenoMax GenoMax • written by sxf520 • sxf520

If you are looking to remove the primer sequences then you can provide these to scan/trim programs like bbduk.sh from BBMap suite or fastp. They should be able to find parts of sequence that are present in your reads. Depending on where the sequence is you can ask the trimmer to remove the relevant match.

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written by GenoMax GenoMax

Thanks. I actually want to know if I should use the full sequence (with the overhang part) or only the gene specific part as the primer sequene.

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written by sxf520 • sxf520

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